Cryo-electron tomography and deep learning denoising reveal native chromatin landscapes of interphase nuclei

Abstract

AbstractThe folding of nucleosome chains influences DNA availability for functional interactions necessary to the regulation of transcription, DNA replication and repair. Despite models based on in vitro studies, the nucleosome chain geometry within the crowded cell nucleus remains elusive. Using cryo-electron tomography and deep learning-based denoising, we directly observed the path of nucleosomal and linker DNA in situ in unstained flash-frozen Drosophila embryos. We quantified linker length and curvature characterizing a disordered zig-zag chromatin folding motif, with a low degree of linker bending. Additionally, nucleosome conformational variability with non-canonical structures and sub-nucleosomal particles were seen as individual objects, without structure averaging, highlighting the high structural heterogeneity of native chromatin.One-Sentence SummaryCryo-ET reveals local zig-zag motifs in interphase chromatin, a range of nucleosome conformations, and sub-nucleosomal particles.